Input and runtime details for job 6527768 (precomputed example)

Sequence input

	sRNA sequences		[.fa]
	Putative target sequences (organism of interest)		[.fa]
	Extract sequences around		start codon
	nt up (1-300)		200
	nt down (1-300)		100

CopraRNA parameters

	Consensus prediction		off
	p-value combination		no
	p-value filtering (0=off)		0

IntaRNA parameters

	Target folding window size		150
	Target max. basepair distance		100

Job ID 6527768 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:24:51 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:20 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:38:58 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:39:05 CET 2018
	Job Completed		@ Fri Feb 16 20:39:38 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6527768&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicA

Output download complete results [zip]

Downloadable files

	CopraRNA result table:		[csv]
	Functional enrichment file		[txt]
	Auxiliary enrichment file		[csv]
	mRNA regions plot		[png] [pdf] [ps]
	sRNA regions plot		[png] [pdf] [ps]
	Functional annotation chart		[html] [pdf]
	Phylogenetic conservation		[png] [pdf]
	16S rDNA tree		[txt] [svg]

mRNA region plot

sRNA region plot

Annot. chart

Conserved, identified interactions for NC_000913 Escherichia coli str. K-12 substr. MG1655

Select: 1-10 11-20 21-30 31-40 41-50 51-60 61-70 71-80 81-90 91-100 101-110 111-120 121-130 131-140 141-150 151-160 161-170 171-180 181-190 191-200 all

Sort by selecting a column name:

Rank	CopraRNA p-value	CopraRNA fdr value	Locus Tag	Gene Name	Energy [kcal/mol]	IntaRNA p-value	Position mRNA	Position sRNA	Annotation
71	0.006638	0.3087	b3857	mobA	-12.61	0.042607	253 -- 264	7 -- 18	molybdopterin-guanine dinucleotide synthase	_____________252__________265\n_____________\|____________\|\n5'-UCC...AGCCA________G___GCGUA...AAC-3'\n______________GACGAAUG_GCG\n______________:\|\|:\|\|\|\|_\|\|\|\n______________UUGUUUAC_CGC\n3'-UUU...UACUA________G___AGAAAG-5'\n_____________\|____________\|\n_____________19___________6\n	254 -- 260	11 -- 17	-15.9619 kcal/mol	2.14186 kcal/mol	1.20891 kcal/mol	252 265@LB@ \| \|@LB@5'-UCC...AGCCA G GCGUA...AAC-3'@LB@ GACGAAUG GCG@LB@ :\|\|:\|\|\|\| \|\|\|@LB@ UUGUUUAC CGC@LB@3'-UUU...UACUA G AGAAAG-5'@LB@ \| \|@LB@ 19 6@LB@@LB@@LB@Energy -12.61 kcal/mol@LB@Hybridization Energy -15.9619 kcal/mol@LB@Unfolding Energy - mRNA 2.14186 kcal/mol@LB@Unfolding Energy - sRNA 1.20891 kcal/mol@LB@@LB@Position - mRNA 253 -- 264@LB@Position - sRNA 7 -- 18@LB@Position Seed - mRNA 254 -- 260@LB@Position Seed - sRNA 11 -- 17@LB@
72	0.006739	0.3087	b2520	yfhM	-8.19	0.237735	190 -- 217	6 -- 30	bacterial alpha2-macroglobulin colonization factor ECAM; anti-host protease defense factor; periplasmic inner membrane-anchored lipoprotein	_____________189__________________________218\n_____________\|____________________________\|\n5'-CUC...GUGGC________AAA____AA____UA_____AGCCG...CUU-3'\n______________AGGGAUGA___AUGA__AAGU__CGCGU\n______________\|\|\|\|\|\|\|\|___\|\|:\|__\|\|:\|__\|\|\|\|\|\n______________UCCCUACU___UAUU__UUUA__GCGCA\n3'-UUU...UUAAG________AC_____G_____C______GAAAG-5'\n_____________\|____________________________\|\n_____________31___________________________5\n	191 -- 197	23 -- 29	-19.496 kcal/mol	3.87755 kcal/mol	7.4255 kcal/mol	189 218@LB@ \| \|@LB@5'-CUC...GUGGC AAA AA UA AGCCG...CUU-3'@LB@ AGGGAUGA AUGA AAGU CGCGU@LB@ \|\|\|\|\|\|\|\| \|\|:\| \|\|:\| \|\|\|\|\|@LB@ UCCCUACU UAUU UUUA GCGCA@LB@3'-UUU...UUAAG AC G C GAAAG-5'@LB@ \| \|@LB@ 31 5@LB@@LB@@LB@Energy -8.19 kcal/mol@LB@Hybridization Energy -19.496 kcal/mol@LB@Unfolding Energy - mRNA 3.87755 kcal/mol@LB@Unfolding Energy - sRNA 7.4255 kcal/mol@LB@@LB@Position - mRNA 190 -- 217@LB@Position - sRNA 6 -- 30@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 23 -- 29@LB@
73	0.006809	0.3087	b4146	epmB	-12.79	0.039583	278 -- 298	1 -- 22	EF-P-Lys34 lysylation protein; weak lysine 2 3-aminomutase	_____________277____________________299\n_____________\|______________________\|\n5'-UUC...GAUCC______ACUUC___________GA-3'\n______________UGAUGA______UGCGUCUUUU\n______________\|\|\|\|:\|______:\|\|\|\|\|\|\|\|:\n______________ACUAUU______GCGCAGAAAG\n3'-UUU...CUACU______GUUUAC__________-5'\n_____________\|_____________________\|\n_____________23____________________1\n	292 -- 298	1 -- 7	-16.8007 kcal/mol	2.75078 kcal/mol	1.25963 kcal/mol	277 299@LB@ \| \|@LB@5'-UUC...GAUCC ACUUC GA-3'@LB@ UGAUGA UGCGUCUUUU@LB@ \|\|\|\|:\| :\|\|\|\|\|\|\|\|:@LB@ ACUAUU GCGCAGAAAG@LB@3'-UUU...CUACU GUUUAC -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -12.79 kcal/mol@LB@Hybridization Energy -16.8007 kcal/mol@LB@Unfolding Energy - mRNA 2.75078 kcal/mol@LB@Unfolding Energy - sRNA 1.25963 kcal/mol@LB@@LB@Position - mRNA 278 -- 298@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 1 -- 7@LB@
74	0.006875	0.3087	b2474	tmcA	-10.30	0.108021	196 -- 222	5 -- 31	elongator methionine tRNA (ac4C34) acetyltransferase	_____________195____________________________223\n_____________\|______________________________\|\n5'-GAU...CGGGG_________C___AC____________U__ACACA...UUG-3'\n______________CAGGGAUGG_UGA__UGAC___UGCGC_UC\n______________\|\|\|\|\|\|\|\|:_\|\|\|__\|:\|\|___\|\|\|\|\|_\|\|\n______________GUCCCUACU_ACU__AUUG___ACGCG_AG\n3'-UUU...CUUAA___________________UUU_____C__AAAG-5'\n_____________\|______________________________\|\n_____________32_____________________________4\n	198 -- 204	23 -- 29	-27.934 kcal/mol	9.88036 kcal/mol	7.7585 kcal/mol	195 223@LB@ \| \|@LB@5'-GAU...CGGGG C AC U ACACA...UUG-3'@LB@ CAGGGAUGG UGA UGAC UGCGC UC@LB@ \|\|\|\|\|\|\|\|: \|\|\| \|:\|\| \|\|\|\|\| \|\|@LB@ GUCCCUACU ACU AUUG ACGCG AG@LB@3'-UUU...CUUAA UUU C AAAG-5'@LB@ \| \|@LB@ 32 4@LB@@LB@@LB@Energy -10.30 kcal/mol@LB@Hybridization Energy -27.934 kcal/mol@LB@Unfolding Energy - mRNA 9.88036 kcal/mol@LB@Unfolding Energy - sRNA 7.7585 kcal/mol@LB@@LB@Position - mRNA 196 -- 222@LB@Position - sRNA 5 -- 31@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 23 -- 29@LB@
75	0.006972	0.3087	b4348	hsdS	-13.63	0.027959	190 -- 211	7 -- 29	specificity determinant for hsdM and hsdR	_____________189_____________________212\n_____________\|_______________________\|\n5'-CUG...UUGGU_______A_____________G_GAAAU...UAA-3'\n______________GGGGUGA_GG_AAUGAGUGCG_G\n______________\|\|\|:\|\|\|_\|:_\|\|::\|:\|\|\|\|_\|\n______________CCCUACU_CU_UUGUUUACGC_C\n3'-UUU...UAAGU_______A__A__________G_AGAAAG-5'\n_____________\|_______________________\|\n_____________30______________________6\n	203 -- 209	9 -- 15	-24.9713 kcal/mol	3.9222 kcal/mol	7.41901 kcal/mol	189 212@LB@ \| \|@LB@5'-CUG...UUGGU A G GAAAU...UAA-3'@LB@ GGGGUGA GG AAUGAGUGCG G@LB@ \|\|\|:\|\|\| \|: \|\|::\|:\|\|\|\| \|@LB@ CCCUACU CU UUGUUUACGC C@LB@3'-UUU...UAAGU A A G AGAAAG-5'@LB@ \| \|@LB@ 30 6@LB@@LB@@LB@Energy -13.63 kcal/mol@LB@Hybridization Energy -24.9713 kcal/mol@LB@Unfolding Energy - mRNA 3.9222 kcal/mol@LB@Unfolding Energy - sRNA 7.41901 kcal/mol@LB@@LB@Position - mRNA 190 -- 211@LB@Position - sRNA 7 -- 29@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 9 -- 15@LB@
76	0.007084	0.3087	b4214	cysQ	-5.34	0.578728	11 -- 17	26 -- 32	3'(2') 5'-bisphosphate nucleotidase	_____________10______18\n_____________\|_______\|\n5'-AAC...AAUCA_______CAUCC...ACA-3'\n______________UCAGGGA\n______________\|\|\|\|\|\|\|\n______________AGUCCCU\n3'-UUU...ACUUA_______ACUAC...AAG-5'\n_____________\|_______\|\n_____________33______25\n	11 -- 17	26 -- 32	-11.6237 kcal/mol	0.931861 kcal/mol	5.35475 kcal/mol	10 18@LB@ \| \|@LB@5'-AAC...AAUCA CAUCC...ACA-3'@LB@ UCAGGGA@LB@ \|\|\|\|\|\|\|@LB@ AGUCCCU@LB@3'-UUU...ACUUA ACUAC...AAG-5'@LB@ \| \|@LB@ 33 25@LB@@LB@@LB@Energy -5.34 kcal/mol@LB@Hybridization Energy -11.6237 kcal/mol@LB@Unfolding Energy - mRNA 0.931861 kcal/mol@LB@Unfolding Energy - sRNA 5.35475 kcal/mol@LB@@LB@Position - mRNA 11 -- 17@LB@Position - sRNA 26 -- 32@LB@Position Seed - mRNA 11 -- 17@LB@Position Seed - sRNA 26 -- 32@LB@
77	0.007102	0.3087	b0832	gsiD	-8.78	0.192254	77 -- 85	7 -- 15	glutathione ABC transporter permease	_____________76________86\n_____________\|_________\|\n5'-UUG...CGUAG_________AUUAC...GAU-3'\n______________AAAUGCGUG\n______________\|\|\|\|\|\|\|:\|\n______________UUUACGCGC\n3'-UUU...UAUUG_________AGAAAG-5'\n_____________\|_________\|\n_____________16________6\n	79 -- 85	7 -- 13	-12.0627 kcal/mol	2.10506 kcal/mol	1.17837 kcal/mol	76 86@LB@ \| \|@LB@5'-UUG...CGUAG AUUAC...GAU-3'@LB@ AAAUGCGUG@LB@ \|\|\|\|\|\|\|:\|@LB@ UUUACGCGC@LB@3'-UUU...UAUUG AGAAAG-5'@LB@ \| \|@LB@ 16 6@LB@@LB@@LB@Energy -8.78 kcal/mol@LB@Hybridization Energy -12.0627 kcal/mol@LB@Unfolding Energy - mRNA 2.10506 kcal/mol@LB@Unfolding Energy - sRNA 1.17837 kcal/mol@LB@@LB@Position - mRNA 77 -- 85@LB@Position - sRNA 7 -- 15@LB@Position Seed - mRNA 79 -- 85@LB@Position Seed - sRNA 7 -- 13@LB@
78	0.007118	0.3087	b1118	lolE	-12.65	0.041861	19 -- 36	6 -- 21	lipoprotein-releasing system transmembrane protein	_____________18_________________37\n_____________\|__________________\|\n5'-CUG...CUACC______CUC_________AACGC...GCA-3'\n______________GGUAAC___GAUGCGCGU\n______________\|:\|\|\|\|___:\|\|\|\|\|\|\|\|\n______________CUAUUG___UUACGCGCA\n3'-UUU...UACUA______U___________GAAAG-5'\n_____________\|__________________\|\n_____________22_________________5\n	30 -- 36	6 -- 12	-20.2716 kcal/mol	6.37224 kcal/mol	1.24519 kcal/mol	18 37@LB@ \| \|@LB@5'-CUG...CUACC CUC AACGC...GCA-3'@LB@ GGUAAC GAUGCGCGU@LB@ \|:\|\|\|\| :\|\|\|\|\|\|\|\|@LB@ CUAUUG UUACGCGCA@LB@3'-UUU...UACUA U GAAAG-5'@LB@ \| \|@LB@ 22 5@LB@@LB@@LB@Energy -12.65 kcal/mol@LB@Hybridization Energy -20.2716 kcal/mol@LB@Unfolding Energy - mRNA 6.37224 kcal/mol@LB@Unfolding Energy - sRNA 1.24519 kcal/mol@LB@@LB@Position - mRNA 19 -- 36@LB@Position - sRNA 6 -- 21@LB@Position Seed - mRNA 30 -- 36@LB@Position Seed - sRNA 6 -- 12@LB@
79	0.007292	0.3087	b0063	araB	-12.45	0.045578	14 -- 28	6 -- 20	L-ribulokinase	_____________13______________29\n_____________\|_______________\|\n5'-CGG...AAGCC________AA_____AACAA...GGU-3'\n______________AUGACAAA__CGCGU\n______________\|\|:\|\|\|\|\|__\|\|\|\|\|\n______________UAUUGUUU__GCGCA\n3'-UUU...ACUAC________AC_____GAAAG-5'\n_____________\|_______________\|\n_____________21______________5\n	15 -- 21	13 -- 19	-14.5023 kcal/mol	0.813134 kcal/mol	1.24244 kcal/mol	13 29@LB@ \| \|@LB@5'-CGG...AAGCC AA AACAA...GGU-3'@LB@ AUGACAAA CGCGU@LB@ \|\|:\|\|\|\|\| \|\|\|\|\|@LB@ UAUUGUUU GCGCA@LB@3'-UUU...ACUAC AC GAAAG-5'@LB@ \| \|@LB@ 21 5@LB@@LB@@LB@Energy -12.45 kcal/mol@LB@Hybridization Energy -14.5023 kcal/mol@LB@Unfolding Energy - mRNA 0.813134 kcal/mol@LB@Unfolding Energy - sRNA 1.24244 kcal/mol@LB@@LB@Position - mRNA 14 -- 28@LB@Position - sRNA 6 -- 20@LB@Position Seed - mRNA 15 -- 21@LB@Position Seed - sRNA 13 -- 19@LB@
80	0.007305	0.3087	b2392	mntH	-9.52	0.145914	200 -- 218	5 -- 21	manganese/divalent cation transporter	_____________199_________________219\n_____________\|___________________\|\n5'-GCU...CACAA_________CUAU______GAGAG...UCG-3'\n______________GAUGACGAA____CGCGUU\n______________\|\|\|:\|\|:\|\|____\|\|\|\|\|:\n______________CUAUUGUUU____GCGCAG\n3'-UUU...UACUA_________AC________AAAG-5'\n_____________\|___________________\|\n_____________22__________________4\n	202 -- 208	13 -- 19	-16.4824 kcal/mol	5.71706 kcal/mol	1.24955 kcal/mol	199 219@LB@ \| \|@LB@5'-GCU...CACAA CUAU GAGAG...UCG-3'@LB@ GAUGACGAA CGCGUU@LB@ \|\|\|:\|\|:\|\| \|\|\|\|\|:@LB@ CUAUUGUUU GCGCAG@LB@3'-UUU...UACUA AC AAAG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -9.52 kcal/mol@LB@Hybridization Energy -16.4824 kcal/mol@LB@Unfolding Energy - mRNA 5.71706 kcal/mol@LB@Unfolding Energy - sRNA 1.24955 kcal/mol@LB@@LB@Position - mRNA 200 -- 218@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 13 -- 19@LB@

Details of Selected Interaction Download Interaction Details

mRNA

sRNA

Energy

Hybridization Energy

Unfolding Energy - mRNA

Unfolding Energy - sRNA

Position - mRNA

Position - sRNA

Position Seed - mRNA

Position Seed - sRNA

Evolutionary conservation of mRNA targets (alignment generated with Jalview)

Evolutionary conservation of sRNA (alignment generated with Jalview)

Job resubmission

Use the following button if you want to resubmit the job with altered input or parameterization:

usability assessment

Please support us by filling this short quality survey for evaluating this

service.

When using CopraRNA please cite :

Patrick R. Wright, Jens Georg, Martin Mann, Dragos A. Sorescu, Andreas S. Richter, Steffen Lott, Robert Kleinkauf, Wolfgang R. Hess, and Rolf Backofen
CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains
Nucleic Acids Research, 2014, 42 (W1), W119-W123.
Patrick R. Wright, Andreas S. Richter, Kai Papenfort, Martin Mann, Joerg Vogel, Wolfgang R. Hess, Rolf Backofen and Jens Georg
Comparative genomics boosts target prediction for bacterial small RNAs
Proc Natl Acad Sci USA, 2013, 110 (37), E3487-E3496.
Martin Raden, Syed M Ali, Omer S Alkhnbashi, Anke Busch, Fabrizio Costa, Jason A Davis, Florian Eggenhofer, Rick Gelhausen, Jens Georg, Steffen Heyne, Michael Hiller, Kousik Kundu, Robert Kleinkauf, Steffen C Lott, Mostafa M Mohamed, Alexander Mattheis, Milad Miladi, Andreas S Richter, Sebastian Will, Joachim Wolff, Patrick R Wright, and Rolf Backofen
Freiburg RNA tools: a central online resource for RNA-focused research and teaching
Nucleic Acids Research, 46(W1), W25-W29, 2018.

Results are computed with CopraRNA version 2.1.2

Main Menu

Freiburg RNA Tools

Interaction Prediction

Seq-Str Alignment

CRISPR

Sequence Design

Splicing

SNP & Mutation

Classification

Gene set extension

MoDPepInt Server

CPSP-Tools Server

Galaxy-FR

CMV server

Teaching